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ABSTRACT:
PROVIDER: PRJEB82503 | ENA |
REPOSITORIES: ENA
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Project description:Purpose: In order to understand the functional significance of sperm transcriptome in stallion fertility, the aim of this study was to generate a detailed body of knowledge about the sperm RNA profile that defines a normal fertile stallion. Methods: The 50 bp single-end ABI SOLiD raw reads were directly aligned with the horse reference sequence EcuCab2 using ABI aligner software (NovoalignCS version 1.00.09, novocraft.com) which uses multiple indexes in the reference genome, identifies candidate alignment locations for each primary read, and allows completion of the alignment. Results: Next generation sequencing (NGS) of total RNA from the sperm of two reproductively normal stallions generated about 70 million raw reads and more than 3 Gb of sequence per sample; over half of these aligned with the EcuCab2 reference genome. Altogether, 19,257 sequence tags with average coverage ≥1 (normalized number of transcripts) were mapped in the horse genome. Conclusion: The sequence of stallion sperm transcriptome is an important foundation for the discovery of transcripts of known and novel genes, and non-coding RNAs, thus improving the annotation of the horse genome sequence draft and providing markers for evaluating stallion fertility.
2013-02-19 | GSE38725 | GEO
Project description:Purpose: In order to understand the functional significance of sperm transcriptome in stallion fertility, the aim of this study was to generate a detailed body of knowledge about the sperm RNA profile that defines a normal fertile stallion. Methods: The 50 bp single-end ABI SOLiD raw reads were directly aligned with the horse reference sequence EcuCab2 using ABI aligner software (NovoalignCS version 1.00.09, novocraft.com) which uses multiple indexes in the reference genome, identifies candidate alignment locations for each primary read, and allows completion of the alignment. Results: Next generation sequencing (NGS) of total RNA from the sperm of two reproductively normal stallions generated about 70 million raw reads and more than 3 Gb of sequence per sample; over half of these aligned with the EcuCab2 reference genome. Altogether, 19,257 sequence tags with average coverage ?1 (normalized number of transcripts) were mapped in the horse genome. Conclusion: The sequence of stallion sperm transcriptome is an important foundation for the discovery of transcripts of known and novel genes, and non-coding RNAs, thus improving the annotation of the horse genome sequence draft and providing markers for evaluating stallion fertility. Reproductively fertile Stallion sperm transcriptome as revealed by RNA sequencing
2013-02-19 | E-GEOD-38725 | biostudies-arrayexpress
Project description:The Origin of a Coastal Indigenous Horse Breed in China Revealed by Genome-Wide SNP Data
2019-03-16 | GSE128374 | GEO
Project description:The Origin of a Coastal Indigenous Horse Breed in China Revealed by Genome-Wide SNP Data
2019-03-16 | GSE128373 | GEO
Project description:The Origin of a Coastal Indigenous Horse Breed in China Revealed by Genome-Wide SNP Data
2019-03-16 | GSE128372 | GEO
Project description:A novel KIT variant in an Icelandic horse with white spotted coat colour
| PRJEB9139 | ENA
Project description:A novel KIT variant in an Icelandic horse with white spotted coat colour
| PRJEB8911 | ENA
Project description:BACKGROUND & AIMS: Ulcerative colitis (UC) is a chronic relapsing inflammatory disorder that affects the colonic epithelium. A combination of genetic and environmental factors is thought to be involved in the pathogenesis, resulting in an abnormal immune response and destruction of the colonic epithelium. In Iceland, the incidence of UC is one of the highest in the world and is three times more common than Crohn’s disease. Previous studies have suggested a genetic component may have an influence on the increased incidence. The aim of this study was to characterise a cohort of patients with UC and identify potential germ line mutations and pathways which could be associated with UC in this population. METHODS: We performed exome sequencing of genomic DNA and genome-wide microarray analysis on macroscopically non-inflamed colonic mucosa from Icelandic patients with UC and age and sexed matched controls. Gene-ontology analysis was used to identify common processes and pathways differentially expressed in tissue from UC cases. Exome sequence data were examined for very rare or novel mutations which might be over represented in the UC cohort. Combined matching of variant analysis and downstream influence on transcriptomic expression in the rectum was also analysed. RESULTS: Non-inflamed colonic tissue from patients with UC demonstrated a significant alteration in the transcriptomic profile compared to controls. Over 2,000 genes were differentially expressed in rectal tissue from UC patients and gene ontology analysis identified an up-regulation in genes associated with cell cycle control and protein processing in the endoplasmic reticulum. Exome sequencing identified two missense mutations in thiopurine S-methyltransferase (TPMT) with a minor allele frequency of 0.22 in the UC patients compared to a reported 0.062 in the Icelandic population and 0.03 in the non-Finnish European populations. A predicted damaging mutation in the inflammatory bowel disease associated gene SLC26A3 was identified which was associated with increased expression of DUOX2 and DUOXA2 in UC rectal tissue. CONCLUSIONS: In patients with UC, the colonic mucosa demonstrates a clear alteration in gene expression compared to control subjects. There is evidence of an elevation in genes involved with cell proliferation and the processing of proteins within the endoplasmic reticulum. Exome sequencing identified an increased prevalence of two damaging TPMT variants within the Icelandic UC population, which would suggest screening the UC population prior to initiation of therapy is warranted in order to avoid the serious toxicity associated with these mutations and azathioprine treatment.
2018-11-01 | GSE105074 | GEO